Hi Kobac.
We have a 1991 Bavaria 38 Lagoon, that like yours, needed upgrading.
The surveyor at the time went to great lengths to point out that the basic boat was of a very high quality and that the internal fittings and joinery was built to a standard that you would not see today unless you paid top dollar. OK the mahogany might not be so fashionable today, but it IS mahogany and finished beautifully.
So we bought the yacht, renewed the standing rigging, engine (new Beta 30), headlining and much of the electronics.
That was about 10 years ago and we would not sell.
I noticed another post noting that the internal panels on some more modern Bavaria yacht tend to flex and creak when under load, this is something I've never come across, even in conditions that, well, more sensible folk would have stayed in harbour.
So good luck in the upgrading, you should end up a very seaworthy and comfortable yacht.